Read and tidy a FASTA file

tidyFasta reads and tidys FASTA file. Use this function as the first step in identifying modification sites.

tidyFasta(path)

Arguments

path	A string of path to a FASTA file.

Value

A data.table with columns named header, sequence, uniprot_ac, uniprot_iso, entry_name.

Examples

tidyFasta("https://www.uniprot.org/uniprot/O13297.fasta")
#>                                                                                                                                        header
#> 1: sp|O13297|CET1_YEAST mRNA-capping enzyme subunit beta OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=CET1 PE=1 SV=2
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 sequence
#> 1: MSYTDNPPQTKRALSLDDLVNHDENEKVKLQKLSEAANGSRPFAENLESDINQTETGQAAPIDNYKESTGHGSHSQKPKSRKSSNDDEETDTDDEMGASGEINFDSEMDFDYDKQHRNLLSNGSPPMNDGSDANAKLEKPSDDSIHQNSKSDEEQRIPKQGNEGNIASNYITQVPLQKQKQTEKKIAGNAVGSVVKKEEEANAAVDNIFEEKATLQSKKNNIKRDLEVLNEISASSKPSKYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSYEIFEGSKKVM
#>    uniprot_ac uniprot_iso entry_name
#> 1:     O13297      O13297 CET1_YEAST